Less than a month prior to Voyager's return, an accidental duplicate returned through an unstable Transwarp conduit, where it began its journey to Earth with the USS Dragon. However, due to the duplication process, the ship and crew began to phase out of existence. The Dragon crew was forced to send her back through the conduit to re-merge with the other Voyager.

After Voyager's return, Ensign Tal Celes transferred to the Dragon-B where she served until her death six months later. Following Janeway's promotion to Admiral, Voyager began to serve in the fleet once again, eventually playing key roles in the Kiklar war and later the attempted foothold by the mirror universe. Her armor technology and transphasic torpedoes were pivotal in defeating the Kiklar.

By 2379Voyager crewman Celes Tal had been assigned to the USS Prometheus engineering department where she developed a tutor/mentor relationship with Master chief petty officer Joshua "Chief" Gunn. When the starship Venture, under the command of Captain Casein Finnegan, went rogue Voyager was assigned (along with the Intrepid and Bellerephon) to assist the Prometheus in the search. ("Shadow Agent")

Fulfilling the alternate-timeline Admiral Kathryn Janeway's words about its fate in the alternate timeline, Voyager became a museum shortly after its return home. ("The Alliance")

However, Voyager was pressed into service as part of a combined Federation/Klingon/Romulan/Dominion Remnant fleet which engaged the Suliban at Sagittarius IX. ("The Ultimate Battle")

Shortly after the battle at Sagittarius IX, Voyager served as "Federation One" (Presidential transport craft) in transporting Federation President Nanietta Bacco to Deep Space 9. ("Honours and Rememberances")

In 2373, in this reality, the Voyager, still under the command of a married Kathryn Janeway, ferried that reality's Scott Fack to the co-ordinates of a Myhr'an super battle cruiser. That reality's Dakota Caldwell served as a Voyager crew member, and he, Fack and Singh transferred to the Myhr'an super battle cruiser in an attempt to stop the M'Tar from conquering the Federation. Making the ultimate sacrifice in battle, Janeway piloted Voyager on a collision course with the Myhr'an super battle cruiser, destroying Voyager and seriously crippling the Myhr'an ship. ("Stranger Than Fiction")